diff picard_FixMateInformation.xml @ 3:52fdfc45590a draft

planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/picard_FixMateInformation.xml	Thu Jul 16 15:32:31 2015 -0400
@@ -0,0 +1,81 @@
+<tool name="FixMateInformation" id="picard_FixMateInformation" version="@TOOL_VERSION@.0">
+  <description>ensure that all mate-pair information is in sync between each read and it's mate pair</description>
+  <macros>
+    <import>picard_macros.xml</import>
+  </macros>
+  <expand macro="requirements" />
+  <command>
+    @java_options@
+    
+    java -jar \$JAVA_JAR_PATH/picard.jar
+    FixMateInformation
+    INPUT="${inputFile}"
+    OUTPUT="${outFile}"
+    ASSUME_SORTED=${assume_sorted}
+    ADD_MATE_CIGAR=${add_mate_cigar}
+    
+    SORT_ORDER=coordinate
+    VALIDATION_STRINGENCY="${validation_stringency}"
+    QUIET=true
+    VERBOSITY=ERROR
+  
+  </command>
+  <inputs>
+    <param name="inputFile" multiple="True" type="data" format="sam,bam" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset"/>
+    <param name="add_mate_cigar" type="boolean" checked="true" truevalue="True" falsevalue="False" label="Adds the mate CIGAR tag (MC) if true, does not if false" help="ADD_MATE_CIGAR; default=True"/>
+    <param name="assume_sorted" type="boolean" truevalue="True" falsevalue="False" label="Assume that the input file is QUERYNAME sorted" help="ASSUME_SORTED; default=False"/>
+ 
+    <expand macro="VS" />
+    
+  </inputs> 
+  
+  <outputs>
+    <data format="bam" name="outFile" label="${tool.name} on ${on_string}: BAM with fixed mates"/>
+  </outputs>
+  
+  <tests>
+    <test>
+      <param name="inputFile" value="picard_FixMateInformation.bam" ftype="bam"/>
+      <param name="add_mate_cigar" value="True"/>
+      <param name="assume_sorted" value="False"/>
+      <param name="validation_stringency" value="LENIENT"/>
+      <output name="outFile" file="picard_FixMateInformation_test1.bam" ftype="bam" lines_diff="2"/>
+    </test>
+  </tests>
+  
+  <stdio>
+    <exit_code range="1:"  level="fatal"/>
+  </stdio>
+  
+  <help>
+
+**Purpose**
+
+Ensure that all mate-pair information is in sync between each read and it's mate pair. Reads marked with the secondary alignment flag are written to the output file unchanged.
+
+------
+
+.. class:: warningmark
+
+**Warning on using ASSUME_SORTED option**
+
+Datasets imported into Galaxy are automatically coordinate sorted. So use this option (set it to True) only if you are sure that this is necessary. If you are not sure - a good rule of thumb
+is to assume that the BAM you are working with is coordinate sorted.
+
+@dataset_collections@
+
+@description@
+
+  ASSUME_SORTED=Boolean
+  AS=Boolean                    If true, assume that the input file is queryname sorted, even if the header says 
+                                otherwise.  Default value: false. 
+  
+  ADD_MATE_CIGAR=Boolean
+  MC=Boolean                    Adds the mate CIGAR tag (MC) if true, does not if false.  Default value: true. 
+  
+@more_info@
+
+  </help>
+</tool>
+
+